feat(qannotate confidence mode): allow the user to specify the homopolymer cutoff

[holmeso]

Description

qannotate's ConfidenceMode was using a hard-coded value to determine if the HOM annotation should be applied to the filter field. This PR allows the user to specify the homopolymer cutoff (via the homCutoff option), with the default value being the same as the previous hard-coded value. This should mean that if you run the code as you would normally, then you will get identical results as before. If you run with the homCutoff value set to something other than the default, you will get different results.

Some formatting has also been performed, and removal of user specific details from qannotate's build.gradle file.

Type of change

• [X] New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Unit tests pass. Code has been run against vcf file, and results verified.

Are WDL Updates Required?

No, assuming that the current defaults are acceptable, yes otherwise

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have made corresponding changes to the documentation
• [X] My changes generate no new warnings
• [X] I have added tests that prove my fix is effective or that my feature works
• [X] New and existing unit tests pass locally with my changes